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Author SHA1 Message Date
Madison Dunitz ae23c9e5b9 white space change to run tests (#2132) 
* update tiledb reqs
 2021-03-30 14:34:39 -05:00
Madison Dunitz 78c9d24ed4 Refactor czi_hosted and server into backend directory, pull common code into backend/common, refactor tests (#2102) 
* move local_server -> backend/server server-> backend/czi_hosted, pull common code into backend/common update imports, tests and make commands
 2021-03-26 00:27:07 -05:00
Madison Dunitz 920d71e6b7 pin numba req (#2110) 
* pin numba req

* make req more flexible
 2021-03-16 11:45:27 -05:00
Madison Dunitz 3b6c46ba86 Fix dependency issues in compatibility tests (#1951) 
* update reqs

* pin scanpy

* merge in fix for race conditions
 2020-10-30 10:47:12 -05:00
Madison Dunitz 946a910ef4 Fix compatibility test (#1948) 
* update anndata version and warning about version

* update compatibility tests
 2020-10-26 17:23:55 -05:00
Madison Dunitz 242546371b Remove Continuous vars with 1 value from histogram, add to info drawer (#1927) 
* remove single val continous metadata from histogram, add to info drawer

* refactor to save singleContinuous values in state

* fix edge case, single continuous values reappeard in rsb when clipped
 2020-10-14 12:46:24 -05:00
Madison Dunitz eb108feb37 Performance test annotations (#1908) 
* make testing plan

* create annotaions sets for different num categories/dataset size

* annotation creation testing

* create scale and perf tests for annotations

* create make commands for tests

* get cell count if not set in test_datasets dict
 2020-10-07 12:36:02 -05:00
Madison Dunitz 998fa4762d run black formatter on repo (#1891) 
* add black to lint make cmd

* add black dependency to installation to push test pipeline
 2020-09-30 11:16:13 -05:00
Madison Dunitzandbmccandless 2ffe5ffcae remove AppFeature and all references to it in the code/tests (#1893) 
* remove AppFeature and all references to it in the code/tests

Co-authored-by: bmccandless <bmccandless@chanzuckerberg.com>
 2020-09-29 18:31:59 -05:00
Madison Dunitz af3c6e1d8e config refactor (#1854) 
* split out config

* add tests for base and app config, refactor client config out of app config

* refactor default config retrieval

* create config test class and helper functions

* move default_config into server to fix import issue
 2020-09-29 16:42:46 -05:00
Madison Dunitz 4f339e89b1 dont cache schema (#1836) 2020-09-15 11:20:00 -05:00
Madison DunitzMadison DunitzmaniarathiSeveriano Badajoz
 		65ea1b673f Dunitz 1685 hosted annotations (#1789) 
* save tiledb array to s3, dont cache user annotations

* Add option to disable annotation filename prompt (#1787)

Co-authored-by: Madison Dunitz <dunitzm@gmail.com>

* set tiledb default context in cxg_adaptor

Co-authored-by: maniarathi <arathi.mani@chanzuckerberg.com>
Co-authored-by: Severiano Badajoz <sbadajoz@chanzuckerberg.com>
 2020-08-24 18:26:08 -05:00
Madison Dunitz b034055c35 update to get_secrets_key (#1755) 
* raise exception when get_secrets fails, get db_uri and set as a default_dataset_config var

* log as info not an error
 2020-08-14 18:17:21 -05:00
Madison Dunitz 6a82030558 remove db_uri secret (#1751) 
* remove db_uri secret

* add test to catch bug in future
 2020-08-14 12:38:46 -05:00
Madison Dunitz 2689d8d2c0 Create hosted user annotations [1685] (#1726) 
* add function to retrieve latest annotation from db, db updates

* read and write tiledb arrays

* adding tests
 2020-08-13 19:07:17 -05:00
Madison Dunitz 80f6137528 retrieve latest annotation from db (#1723) 
* add function to retrieve latest annotation from db, db updates

* dont create directory in s3
 2020-08-11 15:48:12 -05:00
Madison Dunitz f632a8db91 Dunitz/db setup (#1619) 
* initial database setup
 2020-08-03 17:54:06 -05:00
Madison Dunitz d748b9f691 use czi-sci-single-cell-eng github user/access token (#1698) 2020-07-30 15:54:57 -05:00
Madison Dunitz 666e6d9849 Add Deployment hook (#1430) 
* test deployment hook

* remove test branch

* update heroku review deployment
 2020-04-27 13:01:31 -07:00